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Yorodumi- PDB-6x9a: Structure of proline utilization A with trans-4-hydroxy-D-proline... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x9a | ||||||
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Title | Structure of proline utilization A with trans-4-hydroxy-D-proline bound in the L-glutamate-gamma-semialdehyde dehydrogenase active site | ||||||
Components | Bifunctional protein PutA | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / ROSSMANN FOLD / PROLINE DEHYDROGNEASE / ALDEHYDE DEHYDROGENASE / PROLINE CATABOLISM / SUBSTRATE CHANNELING / BIFUNCTIONAL ENZYME | ||||||
Function / homology | Function and homology information proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / cytoplasmic side of plasma membrane / DNA-binding transcription factor activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.41 Å | ||||||
Authors | Tanner, J.J. / Campbell, A.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Arch.Biochem.Biophys. / Year: 2020 Title: Structural analysis of prolines and hydroxyprolines binding to the l-glutamate-gamma-semialdehyde dehydrogenase active site of bifunctional proline utilization A. Authors: Campbell, A.C. / Bogner, A.N. / Mao, Y. / Becker, D.F. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x9a.cif.gz | 951.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x9a.ent.gz | 769 KB | Display | PDB format |
PDBx/mmJSON format | 6x9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x9a_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 6x9a_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6x9a_validation.xml.gz | 103.2 KB | Display | |
Data in CIF | 6x9a_validation.cif.gz | 161.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/6x9a ftp://data.pdbj.org/pub/pdb/validation_reports/x9/6x9a | HTTPS FTP |
-Related structure data
Related structure data | 6x99C 6x9bC 6x9cC 6x9dC 5kf6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 131961.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (strain SM11) (bacteria) Strain: SM11 / Gene: putA, SM11_chr0102 / Production host: Escherichia coli (E. coli) References: UniProt: F7X6I3, proline dehydrogenase, L-glutamate gamma-semialdehyde dehydrogenase |
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-Non-polymers , 7 types, 2540 molecules
#2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Crystallization experiments were set up with SmPutA (6 mg/mL) and trans-4-hydroxy-D-proline (50 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM ...Details: Crystallization experiments were set up with SmPutA (6 mg/mL) and trans-4-hydroxy-D-proline (50 mM) in a buffer containing 50 mM Tris (pH 8.0), 50 mM NaCl, 5% (w/v) glycerol, and 0.5 mM Tris(2-caboxyethyl)phosphine. Crystals were grown using a reservoir solution containing 19% PEG-3350, 0.2 M ammonium sulfate, 0.1 M magnesium chloride, 0.1 M HEPES (pH 8.0), and 0.1 M sodium formate. Cryobuffer: reservoir supplemented with 15 % PEG-200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.41→47.03 Å / Num. obs: 456940 / % possible obs: 96.5 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.038 / Rrim(I) all: 0.071 / Net I/σ(I): 10.7 / Num. measured all: 1532777 / Scaling rejects: 867 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5kf6 Resolution: 1.41→45.98 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.53 Å2 / Biso mean: 22.2189 Å2 / Biso min: 8.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.41→45.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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